############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mixOmics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mixOmics_6.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/mixOmics.Rcheck’ * using R version 4.5.0 RC (2025-04-04 r88126) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘mixOmics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘mixOmics’ version ‘6.32.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... 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only required to store paths of up to 100 bytes and cannot store those of more than 256 bytes, with restrictions including to 100 bytes for the final component. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for sufficient/correct file permissions ... OK * checking whether package ‘mixOmics’ can be installed ... OK * checking installed package size ... INFO installed size is 6.5Mb sub-directories of 1Mb or more: R 1.6Mb data 3.3Mb * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘gsignal’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .plotLoadings_barplot: no visible binding for global variable ‘size.axis’ perf.assess.sgccda: no visible binding for global variable ‘signif.threshold’ plotLoadings.mint.pls: no visible binding for global variable ‘importance’ plotLoadings.mint.pls: no visible binding for global variable ‘color’ plotLoadings.mint.plsda: no visible binding for global variable ‘importance’ plotLoadings.mint.plsda: no visible binding for global variable ‘color’ plotLoadings.mint.spls: no visible binding for global variable ‘importance’ plotLoadings.mint.spls: no visible binding for global variable ‘color’ plotLoadings.mint.splsda: no visible binding for global variable ‘importance’ plotLoadings.mint.splsda: no visible binding for global variable ‘color’ plotLoadings.mixo_pls: no visible binding for global variable ‘importance’ plotLoadings.mixo_plsda: no visible binding for global variable ‘importance’ plotLoadings.mixo_plsda: no visible binding for global variable ‘color’ plotLoadings.mixo_plsda: no visible binding for global variable ‘group’ plotLoadings.mixo_spls: no visible binding for global variable ‘importance’ plotLoadings.mixo_splsda: no visible binding for global variable ‘importance’ plotLoadings.mixo_splsda: no visible binding for global variable ‘color’ plotLoadings.mixo_splsda: no visible binding for global variable ‘group’ plotLoadings.pca: no visible binding for global variable ‘importance’ plotLoadings.rcc: no visible binding for global variable ‘importance’ plotLoadings.rgcca: no visible binding for global variable ‘importance’ plotLoadings.sgcca: no visible binding for global variable ‘importance’ plotLoadings.sgccda: no visible binding for global variable ‘importance’ plotLoadings.sgccda: no visible binding for global variable ‘color’ plotLoadings.sgccda: no visible binding for global variable ‘group’ Undefined global functions or variables: color group importance signif.threshold size.axis * checking Rd files ... NOTE checkRd: (-1) plotLoadings.Rd:479: Lost braces 479 | For code{mint.pls}, \code{mint.spls}: when \code{study="all.partial"}, | ^ * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: perf.Rd: BiocParallelParam-class perf.assess.Rd: BiocParallelParam-class rcc.Rd: estimate.lambda tune.Rd: BiocParallelParam-class tune.block.plsda.Rd: BiocParallelParam-class tune.block.splsda.Rd: BiocParallelParam-class tune.pls.Rd: BiocParallelParam-class tune.plsda.Rd: BiocParallelParam-class tune.spca.Rd: BiocParallelParam-class tune.spls.Rd: BiocParallelParam-class tune.splsda.Rd: BiocParallelParam-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... NOTE S3 methods shown with full name in Rd file 'perf.assess.Rd': ‘perf.assess’ The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed tune.spls 477.472 11.182 501.723 tune.splsda 189.414 5.496 200.091 tune.plsda 94.311 2.574 98.462 tune.pls 80.168 2.039 83.363 tune.block.plsda 76.414 0.435 79.519 perf.assess 51.412 0.853 56.609 plotIndiv 37.897 1.108 41.231 tune.block.splsda 28.986 0.264 101.360 biplot 25.301 0.128 26.758 background.predict 16.896 0.803 18.908 circosPlot 15.974 0.134 18.529 block.splsda 15.394 0.127 16.094 block.spls 12.181 0.102 12.980 tune 10.863 0.432 11.678 pca 9.369 0.077 9.927 tune.mint.splsda 8.192 0.130 8.368 spca 6.586 0.131 6.864 perf 5.306 0.134 5.795 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’